Tapio Salakoski

175 papers A 3B 5C 12Misc 2Journal 62Unranked 86

Year	Rank	Type	Title / Venue / Authors
2023	—	`ch.`	Computing Education Research in Finland. Past, Present and Future of Computing Education Research Lauri Malmi, Arto Hellas, Petri Ihantola, Ville Isomöttönen, Ilkka Jormanainen, Terhi Kilamo, Antti Knutas, Ari Korhonen, Mikko-Jussi Laakso, Sonsoles López-Pernas, Timo Poranen, Tapio Salakoski, Jarkko Suhonen
2022	—	`conf`	Clustering Nursing Sentences - Comparing Three Sentence Embedding Methods. MIE Hans Moen, Henry Suhonen, Sanna Salanterä, Tapio Salakoski, Laura-Maria Peltonen
2022	J	`jnl`	Neural Network and Random Forest Models in Protein Function Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. Kai Hakala, Suwisa Kaewphan, Jari Björne, Farrokh Mehryary, Hans Moen, Martti Tolvanen, Tapio Salakoski, Filip Ginter
2021	—	`conf`	Predictive Models as Early Warning Systems: A Bayesian Classification Model to Identify At-Risk Students of Programming. SAI (2) Ashok Kumar Veerasamy, Mikko-Jussi Laakso, Daryl J. D'Souza, Tapio Salakoski
2021	—	`conf`	Text Classification Model Explainability for Keyword Extraction - Towards Keyword-Based Summarization of Nursing Care Episodes. MedInfo Akseli Reunamo, Laura-Maria Peltonen, Reetta Mustonen, Minttu Saari, Tapio Salakoski, Sanna Salanterä, Hans Moen
2021	J	`jnl`	Universal Lemmatizer: A sequence-to-sequence model for lemmatizing Universal Dependencies treebanks. Nat. Lang. Eng. Jenna Kanerva, Filip Ginter, Tapio Salakoski
2020	J	`jnl`	Assisting nurses in care documentation: from automated sentence classification to coherent document structures with subject headings. J. Biomed. Semant. Hans Moen, Kai Hakala, Laura-Maria Peltonen, Hanna-Maria Matinolli, Henry Suhonen, Kirsi Terho, Riitta Danielsson-Ojala, Maija Valta, Filip Ginter, Tapio Salakoski, Sanna Salanterä
2020	B	`conf`	Entity-Pair Embeddings for Improving Relation Extraction in the Biomedical Domain. ESANN Farrokh Mehryary, Hans Moen, Tapio Salakoski, Filip Ginter
2020	J	`jnl`	Long Term Effects on Technology Enhanced Learning: The Use of Weekly Digital Lessons in Mathematics. Informatics Educ. Einari Kurvinen, Erkki Kaila, Mikko-Jussi Laakso, Tapio Salakoski
2020	C	`conf`	Propagating AI Knowledge Across University Disciplines- The Design of A Multidisciplinary AI Study Module. FIE Samuli Laato, Henna Vilppu, Juho Heimonen, Antti Hakkala, Jari Björne, Ali Farooq, Tapio Salakoski, Antti Airola
2020	J	`jnl`	Supporting the use of standardized nursing terminologies with automatic subject heading prediction: a comparison of sentence-level text classification methods. J. Am. Medical Informatics Assoc. Hans Moen, Kai Hakala, Laura-Maria Peltonen, Henry Suhonen, Filip Ginter, Tapio Salakoski, Sanna Salanterä
2020	C	`conf`	Using early assessment performance as early warning signs to identify at-risk students in programming courses. FIE Ashok Kumar Veerasamy, Daryl J. D'Souza, Mikko-Ville Apiola, Mikko-Jussi Laakso, Tapio Salakoski
2019	—	`conf`	An Unsupervised Query Rewriting Approach Using N-gram Co-occurrence Statistics to Find Similar Phrases in Large Text Corpora. NODALIDA Hans Moen, Laura-Maria Peltonen, Henry Suhonen, Hanna-Maria Matinolli, Riitta Mieronkoski, Kirsi Telen, Kirsi Terho, Tapio Salakoski, Sanna Salanterä
2019	J	`jnl`	Is Multilingual BERT Fluent in Language Generation? CoRR Samuel Rönnqvist, Jenna Kanerva, Tapio Salakoski, Filip Ginter
2019	J	`jnl`	Leveraging Text Repetitions and Denoising Autoencoders in OCR Post-correction. CoRR Kai Hakala, Aleksi Vesanto, Niko Miekka, Tapio Salakoski, Filip Ginter
2019	J	`jnl`	Multilingual is not enough: BERT for Finnish. CoRR Antti Virtanen, Jenna Kanerva, Rami Ilo, Jouni Luoma, Juhani Luotolahti, Tapio Salakoski, Filip Ginter, Sampo Pyysalo
2019	—	`conf`	Template-free Data-to-Text Generation of Finnish Sports News. NODALIDA Jenna Kanerva, Samuel Rönnqvist, Riina Kekki, Tapio Salakoski, Filip Ginter
2019	J	`jnl`	Template-free Data-to-Text Generation of Finnish Sports News. CoRR Jenna Kanerva, Samuel Rönnqvist, Riina Kekki, Tapio Salakoski, Filip Ginter
2019	J	`jnl`	Universal Lemmatizer: A Sequence to Sequence Model for Lemmatizing Universal Dependencies Treebanks. CoRR Jenna Kanerva, Filip Ginter, Tapio Salakoski
2019	—	`conf`	Unsupervised Phrase-Level Query Rewriting for Assisting Search in Clinical Free Text. MedInfo Hans Moen, Laura-Maria Peltonen, Henry Suhonen, Mikko Koivumäki, Tapio Salakoski, Sanna Salanterä
2018	—	`conf`	Biomedical Event Extraction Using Convolutional Neural Networks and Dependency Parsing. BioNLP Jari Björne, Tapio Salakoski
2018	—	`conf`	Evaluation of a Prototype System that Automatically Assigns Subject Headings to Nursing Narratives Using Recurrent Neural Network. Louhi@EMNLP Hans Moen, Kai Hakala, Laura-Maria Peltonen, Henry Suhonen, Petri Loukasmäki, Tapio Salakoski, Filip Ginter, Sanna Salanterä
2018	—	`conf`	Improving Layman Readability of Clinical Narratives with Unsupervised Synonym Replacement. MIE Hans Moen, Laura-Maria Peltonen, Mikko Koivumäki, Henry Suhonen, Tapio Salakoski, Filip Ginter, Sanna Salanterä
2018	J	`jnl`	Potent pairing: ensemble of long short-term memory networks and support vector machine for chemical-protein relation extraction. Database J. Biol. Databases Curation Farrokh Mehryary, Jari Björne, Tapio Salakoski, Filip Ginter
2018	—	`conf`	Turku Neural Parser Pipeline: An End-to-End System for the CoNLL 2018 Shared Task. CoNLL Shared Task (2) Jenna Kanerva, Filip Ginter, Niko Miekka, Akseli Leino, Tapio Salakoski
2018	J	`jnl`	Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling. Database J. Biol. Databases Curation Suwisa Kaewphan, Kai Hakala, Niko Miekka, Tapio Salakoski, Filip Ginter
2017	—	`conf`	A System for Identifying and Exploring Text Repetition in Large Historical Document Corpora. NODALIDA Aleksi Vesanto, Filip Ginter, Hannu Salmi, Asko Nivala, Tapio Salakoski
2017	—	`conf`	Applying BLAST to Text Reuse Detection in Finnish Newspapers and Journals, 1771-1910. ListLang@NoDaLiDa Aleksi Vesanto, Asko Nivala, Heli Rantala, Tapio Salakoski, Hannu Salmi, Filip Ginter
2017	—	`conf`	Creating register sub-corpora for the Finnish Internet Parsebank. NODALIDA Veronika Laippala, Juhani Luotolahti, Aki-Juhani Kyröläinen, Tapio Salakoski, Filip Ginter
2017	—	`conf`	Detecting mentions of pain and acute confusion in Finnish clinical text. BioNLP Hans Moen, Kai Hakala, Farrokh Mehryary, Laura-Maria Peltonen, Tapio Salakoski, Filip Ginter, Sanna Salanterä
2017	—	`conf`	End-to-End System for Bacteria Habitat Extraction. BioNLP Farrokh Mehryary, Kai Hakala, Suwisa Kaewphan, Jari Björne, Tapio Salakoski, Filip Ginter
2017	—	`conf`	Ensemble of Convolutional Neural Networks for Medicine Intake Recognition in Twitter. SMM4H@AMIA Kai Hakala, Farrokh Mehryary, Hans Moen, Suwisa Kaewphan, Tapio Salakoski, Filip Ginter
2016	—	`conf`	Automatically assessed electronic exams in programming courses. ACSW Teemu Rajala, Erkki Kaila, Rolf Lindén, Einari Kurvinen, Erno Lokkila, Mikko-Jussi Laakso, Tapio Salakoski
2016	J	`jnl`	Comparison of automatic summarisation methods for clinical free text notes. Artif. Intell. Medicine Hans Moen, Laura-Maria Peltonen, Juho Heimonen, Antti Airola, Tapio Pahikkala, Tapio Salakoski, Sanna Salanterä
2016	—	`conf`	Deep Learning with Minimal Training Data: TurkuNLP Entry in the BioNLP Shared Task 2016. BioNLP (Shared Task) Farrokh Mehryary, Jari Björne, Sampo Pyysalo, Tapio Salakoski, Filip Ginter
2016	—	`conf`	Factors Affecting the Availability of Electronic Patient Records for Secondary Purposes - A Case Study. WIS Antti Vikström, Sanaz Rahimi Moosavi, Hans Moen, Tapio Salakoski, Sanna Salanterä
2016	—	`conf`	Medical warning system based on Internet of Things using fog computing. IWBIS Iman Azimi, Arman Anzanpour, Amir M. Rahmani, Pasi Liljeberg, Tapio Salakoski
2016	B	`conf`	Programming Misconceptions in an Introductory Level Programming Course Exam. ITiCSE Einari Kurvinen, Niko Hellgren, Erkki Kaila, Mikko-Jussi Laakso, Tapio Salakoski
2016	—	`conf`	Syntactic analyses and named entity recognition for PubMed and PubMed Central - up-to-the-minute. BioNLP@ACL Kai Hakala, Suwisa Kaewphan, Tapio Salakoski, Filip Ginter
2016	—	`conf`	UTU at SemEval-2016 Task 10: Binary Classification for Expression Detection (BCED). SemEval@NAACL-HLT Jari Björne, Tapio Salakoski
2015	J	`jnl`	Application of the EVEX resource to event extraction and network construction: Shared Task entry and result analysis. BMC Bioinform. Kai Hakala, Sofie Van Landeghem, Tapio Salakoski, Yves Van de Peer, Filip Ginter
2015	J	`jnl`	Care episode retrieval: distributional semantic models for information retrieval in the clinical domain. BMC Medical Informatics Decis. Mak. Hans Moen, Filip Ginter, Erwin Marsi, Laura-Maria Peltonen, Tapio Salakoski, Sanna Salanterä
2015	C	`conf`	Comparing student performance between traditional and technologically enhanced programming course. ACE Erkki Kaila, Teemu Rajala, Mikko-Jussi Laakso, Rolf Lindén, Einari Kurvinen, Ville Karavirta, Tapio Salakoski
2015	—	`conf`	Interactive Learning Content for Introductory Computer Science Course Using the ViLLE Exercise Framework. LaTiCE Ville Karavirta, Riku Haavisto, Erkki Kaila, Mikko-Jussi Laakso, Teemu Rajala, Tapio Salakoski
2015	C	`conf`	Learning Low Cost Multi-target Models by Enforcing Sparsity. IEA/AIE Pekka Naula, Antti Airola, Tapio Salakoski, Tapio Pahikkala
2015	J	`jnl`	On study habits on an introductory course on programming. Comput. Sci. Educ. Salla Willman, Rolf Lindén, Erkki Kaila, Teemu Rajala, Mikko-Jussi Laakso, Tapio Salakoski
2015	—	`ch.`	Smart Dosing: A mobile application for tracking the medication tray-filling and dispensation processes in hospital wards. Recent Advances in Ambient Assisted Living N. A. Khan, Natalia Díaz Rodríguez, Riitta Danielsson-Ojala, Hanna Pirinen, Lotta Kauhanen, Sanna Salanterä, Joachim Majors, Sebu Björklund, Kimmo Rautanen, Tapio Salakoski, Ilona Tuominen, Ivan Porres, Johan Lilius
2015	J	`jnl`	TEES 2.2: Biomedical Event Extraction for Diverse Corpora. BMC Bioinform. Jari Björne, Tapio Salakoski
2015	—	`conf`	Towards the Classification of the Finnish Internet Parsebank: Detecting Translations and Informality. NODALIDA Veronika Laippala, Jenna Kanerva, Anna Missilä, Sampo Pyysalo, Tapio Salakoski, Filip Ginter
2014	—	`conf`	Automatic assessment and immediate feedback in first grade mathematics. Koli Calling Einari Kurvinen, Rolf Lindén, Teemu Rajala, Erkki Kaila, Mikko-Jussi Laakso, Tapio Salakoski
2014	J	`jnl`	Building the essential resources for Finnish: the Turku Dependency Treebank. Lang. Resour. Evaluation Katri Haverinen, Jenna Nyblom, Timo Viljanen, Veronika Laippala, Samuel Kohonen, Anna Missilä, Stina Ojala, Tapio Salakoski, Filip Ginter
2014	C	`conf`	Can IT health-care applications improve the medication tray-filling process at hospital wards? An exploratory study using eye-tracking and stress response. Healthcom Natalia Díaz Rodríguez, Johan Lilius, Sebu Björklund, Joachim Majors, Kimmo Rautanen, Riitta Danielsson-Ojala, Hanna Pirinen, Lotta Kauhanen, Sanna Salanterä, Tapio Salakoski, Ilona Tuominen
2014	—	`conf`	Care Episode Retrieval. Louhi@EACL Hans Moen, Erwin Marsi, Filip Ginter, Laura-Maria Murtola, Tapio Salakoski, Sanna Salanterä
2014	—	`conf`	Documentation of the Clinical Phase of the Cardiac Rehabilitation Process in a Finnish University Hospital District. WIS Lotta Kauhanen, Laura-Maria Murtola, Juho Heimonen, Tuija Leskinen, Kari Kalliokoski, Elina Raivo, Tapio Salakoski, Sanna Salanterä
2014	J	`jnl`	Multi-label learning under feature extraction budgets. Pattern Recognit. Lett. Pekka Naula, Antti Airola, Tapio Salakoski, Tapio Pahikkala
2014	—	`conf`	On Evaluation of Automatically Generated Clinical Discharge Summaries. PAHI Hans Moen, Juho Heimonen, Laura-Maria Murtola, Antti Airola, Tapio Pahikkala, Virpi Terävä, Riitta Danielsson-Ojala, Tapio Salakoski, Sanna Salanterä
2014	J	`jnl`	Predicting patient acuity from electronic patient records. J. Biomed. Informatics Elina Kontio, Antti Airola, Tapio Pahikkala, Heljä Lundgrén-Laine, Kristiina Junttila, Heikki Korvenranta, Tapio Salakoski, Sanna Salanterä
2014	—	`conf`	Properties of Object-Level Cross-Validation Schemes for Symmetric Pair-Input Data. S+SSPR Juho Heimonen, Tapio Salakoski, Tapio Pahikkala
2014	J	`jnl`	Statistical parsing of varieties of clinical Finnish. Artif. Intell. Medicine Veronika Laippala, Timo Viljanen, Antti Airola, Jenna Kanerva, Sanna Salanterä, Tapio Salakoski, Filip Ginter
2013	—	`conf`	Building a Large Automatically Parsed Corpus of Finnish. NODALIDA Filip Ginter, Jenna Nyblom, Veronika Laippala, Samuel Kohonen, Katri Haverinen, Simo Vihjanen, Tapio Salakoski
2013	—	`conf`	EVEX in ST'13: Application of a large-scale text mining resource to event extraction and network construction. BioNLP@ACL (Shared Task) Kai Hakala, Sofie Van Landeghem, Tapio Salakoski, Yves Van de Peer, Filip Ginter
2013	—	`conf`	Predicting Conjunct Propagation and Other Extended Stanford Dependencies. DepLing Jenna Nyblom, Samuel Kohonen, Katri Haverinen, Tapio Salakoski, Filip Ginter
2013	—	`conf`	TEES 2.1: Automated Annotation Scheme Learning in the BioNLP 2013 Shared Task. BioNLP@ACL (Shared Task) Jari Björne, Tapio Salakoski
2013	—	`conf`	Towards a Dependency-based PropBank of General Finnish. NODALIDA Katri Haverinen, Veronika Laippala, Samuel Kohonen, Anna Missilä, Jenna Nyblom, Stina Ojala, Timo Viljanen, Tapio Salakoski, Filip Ginter
2013	—	`conf`	UTurku: Drug Named Entity Recognition and Drug-Drug Interaction Extraction Using SVM Classification and Domain Knowledge. SemEval@NAACL-HLT Jari Björne, Suwisa Kaewphan, Tapio Salakoski
2013	—	`conf`	Using Text Mining to Explore Factors Associated with Acute Confusion in Cardiac Patients Documentation. CLEF (Working Notes) Laura-Maria Murtola, Lotta Kauhanen, Hans Moen, Heljä Lundgrén-Laine, Tapio Salakoski, Sanna Salanterä
2013	J	`jnl`	Using cluster analysis to identify weak signals of lethal trends in aviation and healthcare documentation. Int. J. Netw. Virtual Organisations Olli Sjöblom, Laura-Maria Murtola, Juho Heimonen, Lotta Kauhanen, Veronika Laippala, Heljä Lundgrén-Laine, Tapio Salakoski, Sanna Salanterä
2012	J	`jnl`	A Kernel-Based Framework for Learning Graded Relations From Data. IEEE Trans. Fuzzy Syst. Willem Waegeman, Tapio Pahikkala, Antti Airola, Tapio Salakoski, Michiel Stock, Bernard De Baets
2012	—	`conf`	An Ontology to Improve Accessibility and Quality of Patient Instructions. CLEF (Online Working Notes/Labs/Workshop) Juho Heimonen, Tapio Salakoski, Sanna Salanterä
2012	—	`conf`	Avoiding Hazards - What Can Health Care Learn from Aviation? WIS Olli Sjöblom, Juho Heimonen, Lotta Kauhanen, Veronika Laippala, Heljä Lundgrén-Laine, Laura-Maria Murtola, Tapio Salakoski, Sanna Salanterä
2012	B	`conf`	Breaking the Programming Language Barrier: Using Program Visualizations to Transfer Programming Knowledge in One Programming Language to Another. ICALT Johannes Holvitie, Teemu Rajala, Riku Haavisto, Erkki Kaila, Mikko-Jussi Laakso, Tapio Salakoski
2012	—	`conf`	Computer-assisted learning in primary school mathematics using ViLLE education tool. Koli Calling Einari Kurvinen, Rolf Lindén, Teemu Rajala, Erkki Kaila, Mikko-Jussi Laakso, Tapio Salakoski
2012	J	`jnl`	Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology, and Indirect Associations. Adv. Bioinformatics Sofie Van Landeghem, Kai Hakala, Samuel Rönnqvist, Tapio Salakoski, Yves Van de Peer, Filip Ginter
2012	—	`conf`	Implementation and Analysis of Block Dense Matrix Decomposition on Network-on-Chips. HPCC-ICESS Thomas Canhao Xu, Tapio Pahikkala, Antti Airola, Pasi Liljeberg, Juha Plosila, Tapio Salakoski, Hannu Tenhunen
2012	—	`conf`	Parallel Feature Selection for Regularized Least-Squares. PARA Sebastian Okser, Antti Airola, Tero Aittokallio, Tapio Salakoski, Tapio Pahikkala
2012	J	`jnl`	Parallelized Online Regularized Least-Squares for Adaptive Embedded Systems. Int. J. Embed. Real Time Commun. Syst. Tapio Pahikkala, Antti Airola, Thomas Canhao Xu, Pasi Liljeberg, Hannu Tenhunen, Tapio Salakoski
2012	—	`conf`	PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations. BioNLP@HLT-NAACL Jari Björne, Sofie Van Landeghem, Sampo Pyysalo, Tomoko Ohta, Filip Ginter, Yves Van de Peer, Sophia Ananiadou, Tapio Salakoski
2012	J	`jnl`	Semantically linking molecular entities in literature through entity relationships. BMC Bioinform. Sofie Van Landeghem, Jari Björne, Thomas Abeel, Bernard De Baets, Tapio Salakoski, Yves Van de Peer
2012	J	`jnl`	University of Turku in the BioNLP'11 Shared Task. BMC Bioinform. Jari Björne, Filip Ginter, Tapio Salakoski
2012	—	`conf`	VirTu: virtual tutoring environment. Koli Calling Teemu Mäntyharju, Tapio Salakoski, Matti Koivula, Mikko-Jussi Laakso
2012	—	`conf`	Vocabulary In Discharge Documents The Patient's Perspective. CLEF (Online Working Notes/Labs/Workshop) Veronika Laippala, Riitta Danielsson-Ojala, Heljä Lundgrén-Laine, Sanna Salanterä, Tapio Salakoski
2012	J	`jnl`	Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations. Algorithms Mol. Biol. Tapio Pahikkala, Sebastian Okser, Antti Airola, Tapio Salakoski, Tero Aittokallio
2011	—	`conf`	A Dependency-based Analysis of Treebank Annotation Errors. DepLing Katri Haverinen, Filip Ginter, Veronika Laippala, Samuel Kohonen, Timo Viljanen, Jenna Nyblom, Tapio Salakoski
2011	—	`conf`	A Parallel Online Regularized Least-squares Machine Learning Algorithm for Future Multi-core Processors. PECCS Tapio Pahikkala, Antti Airola, Thomas Canhao Xu, Pasi Liljeberg, Hannu Tenhunen, Tapio Salakoski
2011	J	`jnl`	A kernel-based framework for learning graded relations from data CoRR Willem Waegeman, Tapio Pahikkala, Antti Airola, Tapio Salakoski, Michiel Stock, Bernard De Baets
2011	—	`conf`	An Improved Training Algorithm for the Linear Ranking Support Vector Machine. ICANN (1) Antti Airola, Tapio Pahikkala, Tapio Salakoski
2011	J	`jnl`	An experimental comparison of cross-validation techniques for estimating the area under the ROC curve. Comput. Stat. Data Anal. Antti Airola, Tapio Pahikkala, Willem Waegeman, Bernard De Baets, Tapio Salakoski
2011	C	`conf`	Comparing the collaborative and independent viewing of program visualizations. FIE Teemu Rajala, Erkki Kaila, Johannes Holvitie, Riku Haavisto, Mikko-Jussi Laakso, Tapio Salakoski
2011	—	`conf`	EVEX: A PubMed-Scale Resource for Homology-Based Generalization of Text Mining Predictions. BioNLP@ACL Sofie Van Landeghem, Filip Ginter, Yves Van de Peer, Tapio Salakoski
2011	J	`jnl`	Extracting Contextualized Complex Biological Events with Rich Graph-Based Feature Sets. Comput. Intell. Jari Björne, Juho Heimonen, Filip Ginter, Antti Airola, Tapio Pahikkala, Tapio Salakoski
2011	—	`conf`	Fast and parallelized greedy forward selection of genetic variants in Genome-wide association studies. GENSiPS Sebastian Okser, Tapio Pahikkala, Antti Airola, Tero Aittokallio, Tapio Salakoski
2011	—	`conf`	Generalizing Biomedical Event Extraction. BioNLP@ACL (Shared Task) Jari Björne, Tapio Salakoski
2011	—	`conf`	Greedy Regularized Least-Squares for Multi-task Learning. ICDM Workshops Pekka Naula, Tapio Pahikkala, Antti Airola, Tapio Salakoski
2011	—	`conf`	Learning Multi-Label Predictors under Sparsity Budget. SCAI Pekka Naula, Tapio Pahikkala, Antti Airola, Tapio Salakoski
2011	—	`conf`	Learning Valued Relations from Data. Eurofuse Willem Waegeman, Tapio Pahikkala, Antti Airola, Tapio Salakoski, Bernard De Baets
2011	J	`jnl`	On Learning and Cross-Validation with Decomposed Nyström Approximation of Kernel Matrix. Neural Process. Lett. Antti Airola, Tapio Pahikkala, Tapio Salakoski
2011	J	`jnl`	Training linear ranking SVMs in linearithmic time using red-black trees. Pattern Recognit. Lett. Antti Airola, Tapio Pahikkala, Tapio Salakoski
2011	J	`jnl`	U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinform. Yoshinobu Kano, Jari Björne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, K. Bretonnel Cohen, Karin Verspoor, Christophe Roeder, Lawrence E. Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, Thomas Van Parys, Yves Van de Peer, Makoto Miwa, Sophia Ananiadou, Mariana L. Neves, Alberto D. Pascual-Montano, Arzucan Özgür, Dragomir R. Radev, Sebastian Riedel, Rune Sætre, Hong-Woo Chun, Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii
2010	—	`conf`	A comparison of AUC estimators in small-sample studies. MLSB Antti Airola, Tapio Pahikkala, Willem Waegeman, Bernard De Baets, Tapio Salakoski
2010	J	`jnl`	Accuracy of protein hydropathy predictions. Int. J. Data Min. Bioinform. Satu Jääskeläinen, Pentti Riikonen, Tapio Salakoski, Mauno Vihinen
2010	C	`conf`	Applying Permutation Tests for Assessing the Statistical Significance of Wrapper Based Feature Selection. ICMLA Antti Airola, Tapio Pahikkala, Jorma Boberg, Tapio Salakoski
2010	—	`ch.`	Co-Regularized Least-Squares for Label Ranking. Preference Learning Evgeni Tsivtsivadze, Tapio Pahikkala, Jorma Boberg, Tapio Salakoski, Tom Heskes
2010	J	`jnl`	Complex event extraction at PubMed scale. Bioinform. Jari Björne, Filip Ginter, Sampo Pyysalo, Jun'ichi Tsujii, Tapio Salakoski
2010	—	`conf`	Conditional Ranking on Relational Data. ECML/PKDD (2) Tapio Pahikkala, Willem Waegeman, Antti Airola, Tapio Salakoski, Bernard De Baets
2010	—	`conf`	Dependency-Based PropBanking of Clinical Finnish. Linguistic Annotation Workshop Katri Haverinen, Filip Ginter, Timo Viljanen, Veronika Laippala, Tapio Salakoski
2010	C	`conf`	Host-IP Clustering Technique for Deep Web Characterization. APWeb Denis Shestakov, Tapio Salakoski
2010	Misc	`conf`	Host-IP clustering technique for deep web characterization. SAC Denis Shestakov, Tapio Salakoski
2010	J	`jnl`	Learning intransitive reciprocal relations with kernel methods. Eur. J. Oper. Res. Tapio Pahikkala, Willem Waegeman, Evgeni Tsivtsivadze, Tapio Salakoski, Bernard De Baets
2010	—	`conf`	Reconstruction of Semantic Relationships from Their Projections in Biomolecular Domain. BioNLP@ACL Juho Heimonen, Jari Björne, Tapio Salakoski
2010	—	`conf`	Reflections on Koli Calling Conference: emergence of the Koli spirit. Koli Calling Lauri Malmi, Tapio Salakoski
2010	—	`conf`	Scaling up Biomedical Event Extraction to the Entire PubMed. BioNLP@ACL Jari Björne, Filip Ginter, Sampo Pyysalo, Jun'ichi Tsujii, Tapio Salakoski
2010	C	`conf`	Speeding Up Greedy Forward Selection for Regularized Least-Squares. ICMLA Tapio Pahikkala, Antti Airola, Tapio Salakoski
2009	J	`jnl`	Combining hidden Markov models and latent semantic analysis for topic segmentation and labeling: Method and clinical application. Int. J. Medical Informatics Filip Ginter, Hanna Suominen, Sampo Pyysalo, Tapio Salakoski
2009	J	`jnl`	Effects, Experiences and Feedback from Studies of a Program Visualization Tool. Informatics Educ. Erkki Kaila, Teemu Rajala, Mikko-Jussi Laakso, Tapio Salakoski
2009	—	`conf`	Efficient Hold-Out for Subset of Regressors. ICANNGA Tapio Pahikkala, Hanna Suominen, Jorma Boberg, Tapio Salakoski
2009	—	`conf`	Evaluating Pain in Intensive Care. Nursing Informatics Hanna Suominen, Heljä Lundgrén-Laine, Sanna Salanterä, Tapio Salakoski
2009	—	`conf`	Extracting Complex Biological Events with Rich Graph-Based Feature Sets. BioNLP@HLT-NAACL (Shared Task) Jari Björne, Juho Heimonen, Filip Ginter, Antti Airola, Tapio Pahikkala, Tapio Salakoski
2009	—	`conf`	Integrated Data Management and Analysis Environment for Medical Longitudinal Research with Machine Learning Based Prediction Models. CSIE (1) Mika Laaksonen, Barbara Simell, Tapio Salakoski, Olli Simell
2009	—	`conf`	Learning to Extract Biological Event and Relation Graphs. NODALIDA Jari Björne, Filip Ginter, Juho Heimonen, Sampo Pyysalo, Tapio Salakoski
2009	J	`jnl`	Locality kernels for sequential data and their applications to parse ranking. Appl. Intell. Evgeni Tsivtsivadze, Tapio Pahikkala, Jorma Boberg, Tapio Salakoski
2009	J	`jnl`	Matrix representations, linear transformations, and kernels for disambiguation in natural language. Mach. Learn. Tapio Pahikkala, Sampo Pyysalo, Jorma Boberg, Jouni Järvinen, Tapio Salakoski
2009	—	`conf`	Parsing Clinical Finnish: Experiments with Rule-Based and Statistical Dependency Parsers. NODALIDA Katri Haverinen, Filip Ginter, Veronika Laippala, Tapio Salakoski
2009	J	`jnl`	Towards automated processing of clinical Finnish: Sublanguage analysis and a rule-based parser. Int. J. Medical Informatics Veronika Laippala, Filip Ginter, Sampo Pyysalo, Tapio Salakoski
2008	—	`conf`	A Graph Kernel for Protein-Protein Interaction Extraction. BioNLP Antti Airola, Sampo Pyysalo, Jari Björne, Tapio Pahikkala, Filip Ginter, Tapio Salakoski
2008	—	`conf`	A Sparse Regularized Least-Squares Preference Learning Algorithm. SCAI Evgeni Tsivtsivadze, Tapio Pahikkala, Antti Airola, Jorma Boberg, Tapio Salakoski
2008	J	`jnl`	All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning. BMC Bioinform. Antti Airola, Sampo Pyysalo, Jari Björne, Tapio Pahikkala, Filip Ginter, Tapio Salakoski
2008	—	`conf`	Automatic assessment of program visualization exercises. Koli Calling Erkki Kaila, Teemu Rajala, Mikko-Jussi Laakso, Tapio Salakoski
2008	J	`jnl`	Comparative analysis of five protein-protein interaction corpora. BMC Bioinform. Sampo Pyysalo, Antti Airola, Juho Heimonen, Jari Björne, Filip Ginter, Tapio Salakoski
2008	A	`conf`	Correlation of utterance length and segmental duration in Finnish is questionable. INTERSPEECH Jussi Hakokari, Tuomo Saarni, Jouni Isoaho, Tapio Salakoski
2008	B	`conf`	Define and Visualize Your First Programming Language. ICALT Mikko-Jussi Laakso, Erkki Kaila, Teemu Rajala, Tapio Salakoski
2008	J	`jnl`	Detecting biological associations between genes based on the theory of phase synchronization. Biosyst. Chang Sik Kim, Pentti Riikonen, Tapio Salakoski
2008	J	`jnl`	Effectiveness of Program Visualization: A Case Study with the ViLLE Tool. J. Inf. Technol. Educ. Innov. Pract. Teemu Rajala, Mikko-Jussi Laakso, Erkki Kaila, Tapio Salakoski
2008	—	`conf`	Efficient AUC Maximization with Regularized Least-Squares. SCAI Tapio Pahikkala, Antti Airola, Hanna Suominen, Jorma Boberg, Tapio Salakoski
2008	A	`conf`	Investigating perception of places of articulation in sign and speech. INTERSPEECH Stina Ojala, Olli Aaltonen, Tapio Salakoski
2008	—	`ch.`	Kernels for Text Analysis. Advances of Computational Intelligence in Industrial Systems Evgeni Tsivtsivadze, Tapio Pahikkala, Jorma Boberg, Tapio Salakoski
2008	A	`conf`	Utterance-level normalization for relative articulation rate analysis. INTERSPEECH Tuomo Saarni, Jussi Hakokari, Jouni Isoaho, Tapio Salakoski
2007	J	`jnl`	Applying language technology to nursing documents: Pros and cons with a focus on ethics. Int. J. Medical Informatics Hanna Suominen, Tuija Lehtikunnas, Barbro Back, Helena Karsten, Tapio Salakoski, Sanna Salanterä
2007	J	`jnl`	BioInfer: a corpus for information extraction in the biomedical domain. BMC Bioinform. Sampo Pyysalo, Filip Ginter, Juho Heimonen, Jari Björne, Jorma Boberg, Jouni Järvinen, Tapio Salakoski
2007	—	`conf`	Evaluation of Protein Hydropathy Scales. BIBM Satu Jääskeläinen, Pentti Riikonen, Tapio Salakoski, Mauno Vihinen
2007	C	`conf`	Locality Kernels for Protein Classification. WABI Evgeni Tsivtsivadze, Jorma Boberg, Tapio Salakoski
2007	C	`conf`	On Estimating the Scale of National Deep Web. DEXA Denis Shestakov, Tapio Salakoski
2007	—	`conf`	On the unification of syntactic annotations under the Stanford dependency scheme: A case study on BioInfer and GENIA. BioNLP@ACL Sampo Pyysalo, Filip Ginter, Veronika Laippala, Katri Haverinen, Juho Heimonen, Tapio Salakoski
2007	—	`conf`	Role of Different Spectral Attributes in Vowel Categorization: the Case of Udmurt. NODALIDA Janne Savela, Stina Ojala, Olli Aaltonen, Tapio Salakoski
2007	J	`jnl`	Towards automated classification of intensive care nursing narratives. Int. J. Medical Informatics Marketta Hiissa, Tapio Pahikkala, Hanna Suominen, Tuija Lehtikunnas, Barbro Back, Helena Karsten, Sanna Salanterä, Tapio Salakoski
2007	—	`conf`	Utterance-Initial Duration of Finnish Non-Plosive Consonants. NODALIDA Tuomo Saarni, Jussi Hakokari, Olli Aaltonen, Jouni Isoaho, Tapio Salakoski
2006	—	`ed.`	Advances in Natural Language Processing, 5th International Conference on NLP, FinTAL 2006, Turku, Finland, August 23-25, 2006, Proceedings FinTAL Tapio Salakoski, Filip Ginter, Sampo Pyysalo, Tapio Pahikkala
2006	J	`jnl`	Editorial comments. Comput. Sci. Educ. Tapio Salakoski
2006	J	`jnl`	Evaluation of two dependency parsers on biomedical corpus targeted at protein-protein interactions. Int. J. Medical Informatics Sampo Pyysalo, Filip Ginter, Tapio Pahikkala, Jorma Boberg, Jouni Järvinen, Tapio Salakoski
2006	—	`conf`	Implementing a Rule-Based Speech Synthesizer on a Mobile Platform. FinTAL Tuomo Saarni, Jyri Paakkulainen, Tuomas Mäkilä, Jussi Hakokari, Olli Aaltonen, Jouni Isoaho, Tapio Salakoski
2006	—	`conf`	Incorporating External Information in Bayesian Classifiers Via Linear Feature Transformations. FinTAL Tapio Pahikkala, Jorma Boberg, Aleksandr Mylläri, Tapio Salakoski
2006	J	`jnl`	Lexical Adaptation of Link Grammar to the Biomedical Sublanguage: a Comparative Evaluation of Three Approaches CoRR Sampo Pyysalo, Tapio Salakoski, Sophie Aubin, Adeline Nazarenko
2006	—	`conf`	Lexical Adaptation of Link Grammar to the Biomedical Sublanguage: a Comparative Evaluation of Three Approaches. SMBM Sampo Pyysalo, Tapio Salakoski, Sophie Aubin, Adeline Nazarenko
2006	J	`jnl`	Lexical adaptation of link grammar to the biomedical sublanguage: a comparative evaluation of three approaches. BMC Bioinform. Sampo Pyysalo, Tapio Salakoski, Sophie Aubin, Adeline Nazarenko
2006	C	`conf`	Locality-Convolution Kernel and Its Application to Dependency Parse Ranking. IEA/AIE Evgeni Tsivtsivadze, Tapio Pahikkala, Jorma Boberg, Tapio Salakoski
2006	—	`conf`	Regular Approximation of Link Grammar. FinTAL Filip Ginter, Sampo Pyysalo, Jorma Boberg, Tapio Salakoski
2006	—	`conf`	Relevance Ranking of Intensive Care Nursing Narratives. KES (1) Hanna Suominen, Tapio Pahikkala, Marketta Hiissa, Tuija Lehtikunnas, Barbro Back, Helena Karsten, Sanna Salanterä, Tapio Salakoski
2006	—	`conf`	Segmental Duration in Utterance-Initial Environment: Evidence from Finnish Speech Corpora. FinTAL Tuomo Saarni, Jussi Hakokari, Jouni Isoaho, Olli Aaltonen, Tapio Salakoski
2006	—	`conf`	The Vowel Game: Continuous Real-Time Visualization for Pronunciation Learning with Vowel Charts. FinTAL Annu Paganus, Vesa-Petteri Mikkonen, Tomi Mäntylä, Sami Nuuttila, Jouni Isoaho, Olli Aaltonen, Tapio Salakoski
2006	—	`conf`	Towards Automated Classification of Intensive Care Nursing Narratives. MIE Marketta Hiissa, Tapio Pahikkala, Hanna Suominen, Tuija Lehtikunnas, Barbro Back, Helena Karsten, Sanna Salanterä, Tapio Salakoski
2006	J	`jnl`	What about a simple language? Analyzing the difficulties in learning to program. Comput. Sci. Educ. Linda Mannila, Mia Peltomäki, Tapio Salakoski
2005	J	`jnl`	Contextual weighting for Support Vector Machines in literature mining: an application to gene versus protein name disambiguation. BMC Bioinform. Tapio Pahikkala, Filip Ginter, Jorma Boberg, Jouni Järvinen, Tapio Salakoski
2005	Misc	`conf`	Kernels Incorporating Word Positional Information in Natural Language Disambiguation Tasks. FLAIRS Tapio Pahikkala, Sampo Pyysalo, Filip Ginter, Jorma Boberg, Jouni Järvinen, Tapio Salakoski
2005	J	`jnl`	Multi-Perspective Study of Novice Learners Adopting the Visual Algorithm Simulation Exercise System TRAKLA2. Informatics Educ. Mikko-Jussi Laakso, Tapio Salakoski, Linda Grandell, Xuemei Qiu, Ari Korhonen, Lauri Malmi
2005	J	`jnl`	On the visualization of the DNA sequence and its nucleotide content. SIGSAM Bull. Aleksandr Mylläri, Tapio Salakoski, Alexey Pasechnik
2005	B	`conf`	Regularized Least-Squares for Parse Ranking. IDA Evgeni Tsivtsivadze, Tapio Pahikkala, Sampo Pyysalo, Jorma Boberg, Aleksandr Mylläri, Tapio Salakoski
2005	—	`conf`	The Feasibility of Automatic Assessment and Feedback. CELDA Mikko-Jussi Laakso, Tapio Salakoski, Ari Korhonen
2005	—	`conf`	Web Services for DNA Sequence Analysis. DEXA Workshops Denis Shestakov, Tapio Salakoski
2004	—	`conf`	Analysis of Link Grammar on Biomedical Dependency Corpus Targeted at Protein-Protein Interactions. NLPBA/BioNLP Sampo Pyysalo, Filip Ginter, Tapio Pahikkala, Jorma Boberg, Jouni Järvinen, Tapio Salakoski, Jeppe Koivula
2004	—	`conf`	Extracting Protein-Protein Interaction Sentences by Applying Rough Set Data Analysis. Rough Sets and Current Trends in Computing Filip Ginter, Tapio Pahikkala, Sampo Pyysalo, Jorma Boberg, Jouni Järvinen, Tapio Salakoski
2004	J	`jnl`	New Techniques for Disambiguation in Natural Language and Their Application to Biological Text. J. Mach. Learn. Res. Filip Ginter, Jorma Boberg, Jouni Järvinen, Tapio Salakoski
2004	—	`conf`	Ontology-Based Feature Transformations: A Data-Driven Approach. EsTAL Filip Ginter, Sampo Pyysalo, Jorma Boberg, Jouni Järvinen, Tapio Salakoski
2002	J	`jnl`	Mobile access to biological databases on the Internet. IEEE Trans. Biomed. Eng. Pentti Riikonen, Jorma Boberg, Tapio Salakoski, Mauno Vihinen
2001	J	`jnl`	BioWAP, mobile Internet service for bioinformatics. Bioinform. Pentti Riikonen, Jorma Boberg, Tapio Salakoski, Mauno Vihinen
1997	J	`jnl`	Representative noise-free complete-link classification with application to protein structures. Pattern Recognit. Jorma Boberg, Tapio Salakoski
1993	J	`jnl`	General formulation and evaluation of agglomerative clustering methods with metric and non-metric distances. Pattern Recognit. Jorma Boberg, Tapio Salakoski